Eisel enjoyed a 19-year career on the professional circuit, 10 of which were spent alongside Cavendish.
The 38-year-old was a key figure as Cavendish won 20 stages at the Tour de France between 2008 and 2011 at T-Mobile, with the pair also linking up at Team Sky and Dimension Data for more success.
"Genuinely cried reading this," Cavendish wrote on social media in response to Eisel's announcement.
"Closer than teammates, closer than friends, we're brothers. I could never win an argument with you, but I could never win anywhere near the races I have without you. Thank you for all you've done for me, the peloton and cycling. Love you mate."
Eisel fought back from brain surgery in 2018 following a crash at Tirreno-Adriatico and admitted the injury was a factor in his retirement.
"Our sport is an incredible one and has its obvious dangers, and in 2018 I suffered a major injury that could well have brought my career to a premature end," Eisel wrote.
"Not everyone has the good fortune to retire on their own terms and so to have raced for a final season, loving what I do, sees me leave content and proud."
Mark Cavendish (2R) of Team Sky follows the wheel of teammate Bernhard Eisel (R) at the 2012 Tour de France
Image credit: Getty Images
Eisel’s only stage win at a Grand Tour came alongside Cavendish in a team time trial at the 2010 Vuelta.
He also won Paris-Bourges in 2008 and Gent-Wevelgem in 2010.
"Having the opportunity to ride on some of the most prestigious teams in the sport, on the biggest stages of them all, has been an incredible privilege,” he added.
“I have made friends for life and travelled the world living my dream but it's now time to take the next step of my journey."